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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Anthony Nolan Resource Report Resource Website 1+ mentions |
Anthony Nolan (RRID:SCR_004982) | nonprofit organization | Stem cell and bone marrow register in the United Kingdom, managing and recruiting donors internationally for patients who require stem cell transplants. A database of tissue-typing results of all prospective donors is maintained. A national cord blood program consisting of both a cord blood bank and a research institute provides donated umbilical cord blood for use in clinical transplants and research. Research is conducted in immunogenetics, immunotherapy, bioinformatics (curating the World Health Organisation HLA Nomenclature database, ensuring that all new tissue types are consistently documented), and immune reconstitution. | cord blood, stem cell, blood stem cell, bone marrow, transplant, register | is parent organization of: Anthony Nolan Research Institute | Blood cancer | grid.426412.7, Wikidata: Q4773196, nlx_97115, ISNI: 0000 0004 0623 6380 | https://ror.org/043bfms20 | SCR_004982 | Anthony Nolan UK blood cancer charity, Anthony Nolan Trust | 2026-08-01 12:02:47 | 4 | |||||||
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Medical University of Vienna Institute of Neurology Resource Report Resource Website |
Medical University of Vienna Institute of Neurology (RRID:SCR_005030) | MedUni Vienna IN | institution | The (Clinical) Institute of Neurology (IN) of the Medical University Vienna was founded in 1882 by Heinrich Obersteiner. It is the oldest institution embracing the multidisciplinarity of neurosciences and has served as model for the establishment of similarly designed institutions in many countries. The original location of the then Neurological Institute in Vienna was at Schwarzspanierstrasse. Since 1993, IN is located in the Vienna General Hospital in top-class laboratory facilities. IN is committed to its proud tradition as Obersteiner Institute and to a promising future of a nationally and internationally leading institution in the clinical neurosciences. Our work aims to translate the understanding of nervous diseases to the development of novel therapeutics and diagnostics. IN''''s tasks include diagnostic patient service, research and graduate / postgraduate teaching in neuropathology, neurochemistry, and neuro-molecular biology in an integrated way. Neuropathology is a recognized medical specialty in Austria. It analyzes structural changes of nervous tissues in disease. Diagnostic neuropathology makes use of most modern morphological techniques applied to diseased central, peripheral and vegetative nervous tissues and fluids, and muscle. Neuropathological diagnoses are a basis for disease classification and rational therapies. Neurodegenerative disorders, in particular prion diseases, virus diseases affecting the nervous system, and brain tumors (neuro-oncology) are research priorities. In the highly publicized area of prion diseases, IN has developed into a national and international center of excellence and expertise that leads several European, EU-funded networks in prion research. As an indispensable asset, the IN possesses a large brain bank that has systematically collected neuropathological specimens since 1948. Most samples are fixed and paraffin-embedded tissue only, but in a part of neurosurgical, nerve and muscle biopsies and autopsies, also fresh tissue is obtained, frozen and stored at -80 degrees C. Occasionally blood and CSF are also available. The unique neuropathological collection of histological slides, paraffin blocks and formol-fixed nervous tissues now comprises about 16.000 brain autopsies, 30.000 neurosurgical and 7.500 nerve/muscle biopsies. Also a number of cell cultures have been stored, mainly fibroblasts from patients with rare neurometabolic diseases, and primary cultures of brain tumors. IN participates in the EU-supported European Network of Brain Banks BrainNet Europe. | neurodegenerative disease, prion disease, neuroviral disease, neurometabolic disease, brain tumor, nervous system disease, neuropathology, nervous system, neuro-oncology, clinical, neuroscience, clinical neuroscience, tissue, brain tissue, brain, blood, cerebral spinal fluid, cell, fibroblast, brain tumor, tumor, fixed, paraffin-embedded, fresh, frozen, histological slide, paraffin block, formol-fixed, neuropathological specimen, nerve, muscle |
is listed by: One Mind Biospecimen Bank Listing is related to: BrainNet Europe has parent organization: Medical University of Vienna; Vienna; Austria |
Neurodegenerative disease, Prion Disease, Neuroviral disease, Neurometabolic disease, Brain tumor, Nervous system disease, Neuropathological specimen | nlx_144015 | SCR_005030 | Vienna Brain Bank, Vienna Institute of Neurology | 2026-08-01 12:02:48 | 0 | |||||||
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BEERS Resource Report Resource Website 10+ mentions |
BEERS (RRID:SCR_005090) | BEERS | software resource | A simulation engine for generating RNA-Seq data that was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data. By default BEERS simulates either mouse or human paired-end RNA-Seq data modeled on the illumina platform. It starts with a large number of gene models (approx 500K) taken from about ten different published annotation efforts, and then chooses a fixed number of these genes at random (30,000 by default). This avoids biasing for or against any particular set of annotations. BEERS then introduces substitutions, indels, alternate spice forms, sequencing errors, and intron signal. BEERS can also simulate strand specific reads. BEERS does not simulate quality scores. There are four configuration files required, these are available for human and mouse. BEERS can also be configured to use any set of gene models. Pre-built indexes for human refseq are given. Using these indexes will generate a much tamer set of transcripts. BEERS is written in perl. | perl, rna-seq |
is listed by: OMICtools has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA |
PMID:21775302 | OMICS_01364 | SCR_005090 | Benchmarker for Evaluating the Effectiveness of RNA-Seq Software (BEERS), Benchmarker for Evaluating the Effectiveness of RNA-Seq Software | 2026-08-01 12:02:54 | 22 | |||||||
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AnnTools Resource Report Resource Website 1+ mentions |
AnnTools (RRID:SCR_005170) | AnnTools | software resource | Software tool for annotating single nucleotide substitutions (SNP/SNV), small insertions/deletions (indels), and copy number variations (CNV) calls generated from sequencing and microarray data. Only human genome build 37/hg19 can be annotated at this time. | single nucleotide substitution, snp, snv, indel, copy number variation, sequencing, microarray, linux, unix, mac osx, python, mysql, genome annotation, genome, annotation |
is listed by: OMICtools has parent organization: SourceForge |
BSD License | OMICS_00166 | SCR_005170 | 2026-08-01 12:02:50 | 4 | ||||||||
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PathSeq Resource Report Resource Website 50+ mentions |
PathSeq (RRID:SCR_005203) | PathSeq | software resource | A computational tool for the identification and analysis of microbial sequences in high-throughput human sequencing data that is designed to work with large numbers of sequencing reads in a scalable manner. This process is composed of a subtractive phase in which input reads are subtracted by alignment to human reference sequences, and an analytic phase in which the remaining reads are aligned to microbial reference sequences (viral, fungal, bacterial, archaeal) and de novo assembled. PathSeq is currently available in a cloud computing environment via Amazon Web Services The typical approach one would take to pathogen discovery with PathSeq: RNA or DNA is extracted from the tissue of interest and sequencing libraries are constructed to be run on the next-generation DNA sequencing platform of choice. The resulting sequence data is run through the PathSeq pipeline in a cloud computing environment. PathSeq reports potential microbes in the sequence data as well as the complete set of reads that could not be identified as human or microbial sequences. | virus, microbe, pathogen, dna, rna, next-generation sequencing |
is listed by: OMICtools is related to: Amazon Web Services has parent organization: Broad Institute |
PMID:21552235 | Acknowledgement requested, Account required, (for Amazon Web Services and you will need to pay for the AWS resource time) | OMICS_00221 | SCR_005203 | PathSeq: Pathogen Discovery | 2026-08-01 12:02:57 | 62 | ||||||
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READSCAN Resource Report Resource Website 1+ mentions |
READSCAN (RRID:SCR_005204) | READSCAN | software resource | A highly scalable parallel software program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. | pathgen, genome, sequence, high-throughput sequence, align, read, host, microbe, virus, taxon, simulation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: King Abdullah University of Science and Technology; Makkah Province; Saudi Arabia |
PMID:23193222 | OMICS_00222, biotools:readscan | https://bio.tools/readscan | SCR_005204 | 2026-08-01 12:02:47 | 5 | |||||||
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VirusSeq Resource Report Resource Website 10+ mentions |
VirusSeq (RRID:SCR_005206) | VirusSeq | software resource | An algorithmic software tool for detecting known viruses and their integration sites using next-generation sequencing of human cancer tissue. VirusSeq takes FASTQ files (paired-end reads) as input. | next-generation sequencing, virus, integration site, cancer tissue, genome, rna-seq, whole genome sequencing, fastq, paired-end read, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Texas MD Anderson Cancer Center |
Cancer | OMICS_00227, biotools:virusseq | https://bio.tools/virusseq | SCR_005206 | 2026-08-01 12:02:57 | 23 | |||||||
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Oklahoma Medical Research Foundation Resource Report Resource Website 50+ mentions |
Oklahoma Medical Research Foundation (RRID:SCR_005287) | OMRF | institution | A biomedical research institute that aims to understand and develop more effective treatments for human disease, focusing on critical research areas such as heart disease, cancer, lupus and Alzheimer's disease. | human disease, cardiovascular disease, cancer, lupus, alzheimer’s disease, treatment, biomedical research institute |
is parent organization of: C. elegans Gene Knockout Consortium is parent organization of: Oklahoma Medical Research Foundation OMRF Clinical Genomics Center Core Facility |
Heart disease, Cancer, Lupus, Alzheimer's disease | Public | grid.274264.1, ISNI: 0000 0000 8527 6890, Wikidata: Q7082264, nlx_144327, Crossref funder ID: 100008907 | https://ror.org/035z6xf33 | SCR_005287 | 2026-08-01 12:02:49 | 60 | ||||||
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WHAM Resource Report Resource Website 100+ mentions |
WHAM (RRID:SCR_005497) | WHAM | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. High-throughput sequence alignment tool that aligns short DNA sequences (reads) to the whole human genome at a rate of over 1500 million 60bps reads per hour, which is one to two orders of magnitudes faster than the leading state-of-the-art techniques. Feature list for the current version (v 0.1.5) of WHAM: * Supports paired-end reads * Supports up to 5 errores * Supports alignments with gaps * Supports quality scores for filtering invalid alignments, and sorting valid alignments * finds ALL valid alignments * Supports multi-threading * Supports rich reporting modes * Supports SAM format output | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
Facebook ; NSF IIS-1110948 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00697, biotools:wham | https://bio.tools/wham, https://sources.debian.org/src/wham-align/ | SCR_005497 | Wisconsin?s High-throughput Alignment Method | 2026-08-01 12:02:55 | 345 | |||||
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Allen Institute Resource Report Resource Website 50+ mentions |
Allen Institute (RRID:SCR_005435) | institution | Non profit bioscience research organization in Seattle, Washington dedicated to accelerating research globally and sharing that data within the science community. Allen Institute for Brain Science, Allen Institute for Cell Science, Allen Institute for Immunology, and The Paul G. Allen Frontiers Group are four divisions of this Institute with commitment to open science model within its research institutes. | organization, brain, health, disease, research, human, mouse, dataset, cell, immunology, data, map |
is related to: scrattch taxonomy is parent organization of: Allen Institute for Brain Science is parent organization of: Allen Brain Atlas is parent organization of: Allen Human Reference Atlas, 3D, 2020 is parent organization of: Scrattch.Hicat is parent organization of: COVID-19 Open Research Dataset is parent organization of: CORD-19 Explorer is parent organization of: CellLocator is parent organization of: Allen Mouse Brain Common Coordinate Framework is parent organization of: Common Cell Type Nomenclature is parent organization of: Smart-seq2 Single Nucleus Multi Sample Pipeline is parent organization of: BICCN is parent organization of: Allen Cell and Structure Segmenter is parent organization of: Allen Brain Cell Atlas is parent organization of: BRAIN Initiative Cell Atlas Network is parent organization of: MapMyCells is parent organization of: Genetic Tools Atlas is parent organization of: Annotation Comparison Explorer is parent organization of: BioFile Finder is parent organization of: HMBA Adult Human Brain Atlas is parent organization of: Harmonized Ontology of Mammalian Brain Anatomy (HOMBA) |
nlx_144532, Wikidata:Q24191489, grid.507729.e | https://ror.org/03cpe7c52 | SCR_005435 | The Allen Institute | 2026-08-01 12:02:52 | 55 | ||||||||
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JEPETTO Resource Report Resource Website 10+ mentions |
JEPETTO (RRID:SCR_005909) | JEPETTO | software resource | A Cytoscape plugin that performs integrated gene set analysis using information from interaction, pathways and processes databases. The plugin integrates information from three separate web servers specializing in enrichment analysis, pathways expansion and topological matching. It uses the TopoGSA server to identify topological analogies between the user selected gene set and the known pathways and processes. TopoGSA finds the most similar biological mechanism using the topological features of the interaction network of a user selected gene set. It is also able to suggest genes related to the query gene set using two pathway analysis servers EnrichNet and PathExpand. Both these servers are using a different topological matching algorithms that extends the query gene set with genes from the pathway databases. This integration substantially simplifies the analysis of user gene sets and the interpretation of the results. | gene set enrichment analysis, topological analysis, interaction network, java, enrichment analysis, functional analysis, gene prioritization, integrated analysis, network analysis, interaction, pathway, process, topology, gene |
is listed by: OMICtools has parent organization: Cytoscape has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom |
PMID:24363376 | GNU General Public License | OMICS_02247 | SCR_005909 | Java Enrichment of Pathways Extended To Topology | 2026-08-01 12:03:00 | 15 | ||||||
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Mental Illness Research Education and Clinical Center Resource Report Resource Website |
Mental Illness Research Education and Clinical Center (RRID:SCR_006956) | MIRECC | institution | The Mental Illness Research, Education and Clinical Centers (MIRECC) were established by Congress with the goal of researching the causes and treatments of mental disorders and using education to put new knowledge into routine clinical practice in the VA. Congress established MIRECCs in October 1996 through Public Law 104-262. There are currently 10 MIRECCs. Each MIRECC focuses on mental illnesses or conditions that are common in Veterans. MIRECCs investigate the causes of mental illness, develop new treatments for mental illness, and evaluate both established and new treatments with the goal of identifying best practices. The MIRECCs also develop educational and training initiatives to implement best practices into the clinical settings of the VA. Each MIRECC works with all the facilities in its network (region) on research, education and clinical initiatives, evaluating services offered to the Veteran and helping the networks implement improved treatments, services, or practices. Several educational products are posted on this site on the Products page. These materials are in the public domain and available for your use. Many MIRECCs have additional materials that can be downloaded from their web sites or are available by request. | mental disease | has parent organization: U.S. Department of Veterans Affairs | nlx_143947, grid.453170.4, Crossref funder ID: 100006812, ISNI: 0000 0004 0464 759X | https://ror.org/02hd1sz82 | SCR_006956 | 2026-08-01 12:03:24 | 0 | ||||||||
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Alzheimers Association Resource Report Resource Website 100+ mentions |
Alzheimers Association (RRID:SCR_007398) | ALZ | nonprofit organization | A non profit organization dedicated to providing support for patients and families with Alzheimer's disease, to educating the public about the disease, to funding a wide range of Alzheimer's disease related research and to finding ways to treat and eventually to prevent Alzheimer's disease. Resources include: the Alzheimer's Association Green-Field Library, a research grants program, and the Journal of the Alzheimer's Association. | advocacy group, brain, brain health, clinical, dementia, alzheimers disease, community building portal, narrative resource, training material, database, training resource, service resource, FASEB list |
is related to: ADNI - Alzheimer's Disease Neuroimaging Initiative is related to: International Genomics of Alzheimers Project is parent organization of: General Practitioner Assessment of Cognition is parent organization of: Alzheimers Association Research Roundtable is parent organization of: Biomarkers Across Neurodegenerative Diseases is parent organization of: Alzheimer's Association International Research Grant Program is parent organization of: Informant Questionnaire on Cognitive Decline in the Elderly is parent organization of: IADRP is parent organization of: CADRO |
Alzheimer's disease, Aging | Public, Available to the research community | ISNI: 0000 0004 0614 7003, nif-0000-00451, Crossref funder ID: 100000957, grid.422384.b, Wikidata: Q4738818 | https://ror.org/0375f4d26 | SCR_007398 | Alzheimers Association, Alzheimer's Association | 2026-08-01 12:03:34 | 114 | |||||
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Association for Research in Vision and Ophthalmology Resource Report Resource Website 10+ mentions |
Association for Research in Vision and Ophthalmology (RRID:SCR_007400) | ARVO | nonprofit organization | An eye and vision research organization whose goal is to encourage and assist research, training, publication, and dissemination of knowledge in vision and ophthalmology. ARVO membership is comprised of more than 11,500 individuals. Some 42% of members reside in over 70 countries outside the U.S. The membership is multidisciplinary and consists of both clinical and basic researchers (approximately 44% MD/Ophthalmologists, 26% PhDs, and 30% Other, including optometrists, osteopaths, and veterinarians). ARVO is governed by a Board of Trustees, who are elected from candidates put forth by the 13 Scientific Sections. | vision, ophthalmology, research, organization portal, topical portal | nif-0000-00457, grid.432636.6, ISNI: 0000 0001 0944 6445, Crossref funder ID: 100005426 | https://ror.org/033523d69 | SCR_007400 | 2026-08-01 12:03:29 | 16 | |||||||||
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Cancer Registry of Norway Resource Report Resource Website 1+ mentions |
Cancer Registry of Norway (RRID:SCR_008879) | Cancer Registry of Norway | institution | Comprises 3 registries of cancer patients in Norway: the Incidence Registry, the Clinical Registry and Cancer Statistics. The Incidence Registry contains the basic data items collected from clinicians and pathologists, as well as from administrative discharge and mortality sources. It is updated continuously with information on both new cases, as well as cases diagnosed in previous years. All medical doctors in the country are instructed by law to notify new cancer cases. Clinical Registries: Registration of treatment and follow-up of Norwegian cancer patients. Clinical registries comprehensive registration schemes dedicated to specific cancers have been established to include detailed information on diagnostic measures, therapy, and follow-up. Cancer Statistics: Database of cancer statistics. The Cancer Registry of Norway is maintained by the Institute of Population-based Cancer Research and established in 1951. It is one of the oldest national cancer registries in the world. This, combined with the unique personal identification number used in Norway, makes the Cancer Registry''s data suitable, also internationally; by establishing new knowledge through research and spreading information on cancer. | is parent organization of: Janus Serum Bank | Cancer, Breast cancer, Cervical cancer, Colorectal cancer, Prostate cancer, Lung cancer, Hereditary cancer, Pediatric solid tumor, Ovarian cancer, Malignant melanoma | grid.418941.1, ISNI: 0000 0001 0727 140X, nlx_149447 | https://ror.org/03sm1ej59 | SCR_008879 | Cancer Registry of Norway: Institute of Population-based Cancer Research | 2026-08-01 12:04:06 | 6 | |||||||
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ANTsR Resource Report Resource Website 10+ mentions |
ANTsR (RRID:SCR_008891) | ANTsR | software resource | An R extension to ANTs that performs multivariate statistical parametric mapping of DTI, T1 and other datatypes for the purpose of both performing clinical studies and for tracking the performance of ANTs (and other) image processing methodologies. ANTsR depends upon the R statistical language, bash scripts and the ANTs toolkit. Some branches of ANTsR will also depend upon pipedream and specific datasets. Some of these datasets will be open access and, in that case, ANTsR will provide a 100% reproducible neuroimaging study on that data. | neuroimaging, multivariate statistical parametric mapping, dti, t1, image processing, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ANTS - Advanced Normalization ToolS |
BSD License | nlx_151365 | SCR_008891 | 2026-08-01 12:04:06 | 47 | ||||||||
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Fisher BioServices Resource Report Resource Website 100+ mentions |
Fisher BioServices (RRID:SCR_010528) | Fisher BioServices | commercial organization | Biological material management services provider including biospecimen storage, biobanking services, specimen collection kits, sample processing, DNA /RNA extraction and amplification, sample storage, distribution, and clinical trial support. They also offer transport and storage of active pharmaceutical ingredient(s) (API and bio-API), including cryogenic. They can assist with public health research, phase I???????????????IV studies, prospective and retrospective studies, IND/NDA submissions to the FDA, and entry of biotherapeutics into the commercial marketplace. | blood, blood derivative, plasma, pbmc, buffy coat, serum, saliva, cerebrospinal fluid, fluid, urine, urethral swab, breast milk, meconium, nail clipping, hair, semen, cervical swab, microorganism, plant matter, chemical, marine organism, cell line, stem cell, disease research, clinical trial, drug, biologic therapeutic | is listed by: One Mind Biospecimen Bank Listing | nlx_22160, grid.281207.e, ISNI: 0000 0004 1796 1094 | https://ror.org/041mbwk52 | http://www.cryonix.com/ | SCR_010528 | 2026-08-01 12:04:14 | 396 | |||||||
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Surgical Biologics - a MiMedx Group Company Resource Report Resource Website |
Surgical Biologics - a MiMedx Group Company (RRID:SCR_010661) | commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 2nd, 2022. Tissue bank and service organization for bioimplants. | implant | is listed by: One Mind Biospecimen Bank Listing | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_69747 | http://www.surgicalbiologics.com | SCR_010661 | Surgical Biologics, Surgical Biologics Inc. | 2026-08-01 12:04:15 | 0 | |||||||
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Advanced Biohealing, Inc. Resource Report Resource Website |
Advanced Biohealing, Inc. (RRID:SCR_010630) | ABH | commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 2nd, 2022. Manufacturer of Dermagraft, a bio-engineered skin substitute that assists in restoring damaged tissue and supports the body's natural healing process. | is listed by: One Mind Biospecimen Bank Listing | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_60088 | SCR_010630 | Advanced BioHealing, Advanced Biohealing Inc. | 2026-08-01 12:04:15 | 0 | ||||||||
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NHLBI Grand Opportunity Exome Sequencing Project Resource Report Resource Website 10+ mentions |
NHLBI Grand Opportunity Exome Sequencing Project (RRID:SCR_010798) | NHLBI GO ESP, GO ESP | knowledge environment | Project focused on understanding the contribution of rare genetic variation to heart, lung and blood disorders through the sequencing of well-phenotyped populations. | next-generation sequencing, protein coding region, human, genome, phenotype, exome sequencing |
is listed by: OMICtools has parent organization: University of Washington; Seattle; USA |
NHLBI RC2 HL-103010; NHLBI RC2 HL-102923; NHLBI RC2 HL-102924; NHLBI RC2 HL-102925; NHLBI RC2 HL-102926 |
OMICS_00277 | SCR_010798 | NHLBI Grand Opportunity Exome Sequencing Project (ESP), NHLBI GO Exome Sequencing Project (ESP) | 2026-08-01 12:04:16 | 31 |
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